data_X0O
# 
_chem_comp.id                                    X0O 
_chem_comp.name                                  "[[(2~{R},3~{S},4~{R},5~{S})-5-(4-azanyl-1-methyl-2-oxidanylidene-pyrimidin-5-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" 
_chem_comp.type                                  "RNA linking" 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C10 H18 N3 O14 P3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-05-25 
_chem_comp.pdbx_modified_date                    2023-12-22 
_chem_comp.pdbx_ambiguous_flag                   N 
_chem_comp.pdbx_release_status                   REL 
_chem_comp.pdbx_replaced_by                      ? 
_chem_comp.pdbx_replaces                         ? 
_chem_comp.formula_weight                        497.183 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     X0O 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        8SY7 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.alt_atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.charge 
_chem_comp_atom.pdbx_align 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_leaving_atom_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_chem_comp_atom.model_Cartn_x 
_chem_comp_atom.model_Cartn_y 
_chem_comp_atom.model_Cartn_z 
_chem_comp_atom.pdbx_model_Cartn_x_ideal 
_chem_comp_atom.pdbx_model_Cartn_y_ideal 
_chem_comp_atom.pdbx_model_Cartn_z_ideal 
_chem_comp_atom.pdbx_component_atom_id 
_chem_comp_atom.pdbx_component_comp_id 
_chem_comp_atom.pdbx_ordinal 
X0O C14 C1  C 0 1 N N N N N N 132.155 146.073 131.767 -0.822 1.888  0.431  C14 X0O 1  
X0O C15 C2  C 0 1 N N R N N N 131.087 145.930 132.645 -1.884 1.677  -0.651 C15 X0O 2  
X0O C16 C3  C 0 1 N N S N N N 131.458 146.531 134.071 -3.102 2.603  -0.407 C16 X0O 3  
X0O C17 C4  C 0 1 N N R N N N 130.918 145.794 134.904 -4.240 1.839  -1.127 C17 X0O 4  
X0O C18 C5  C 0 1 N N S N N N 130.457 144.388 134.133 -3.724 0.389  -1.215 C18 X0O 5  
X0O C19 C6  C 0 1 N N N N N N 131.156 143.216 134.780 -4.685 -0.540 -0.521 C19 X0O 6  
X0O C20 C7  C 0 1 N N N N N N 130.828 142.802 136.304 -4.894 -0.445 0.870  C20 X0O 7  
X0O C22 C8  C 0 1 N N N N N N 132.383 141.035 136.181 -6.404 -2.191 0.759  C22 X0O 8  
X0O C24 C9  C 0 1 N N N N N N 133.700 140.700 133.855 -6.972 -3.320 -1.319 C24 X0O 9  
X0O C25 C10 C 0 1 N N N N N N 132.167 142.429 134.011 -5.366 -1.476 -1.224 C25 X0O 10 
X0O N21 N1  N 0 1 N N N N N N 131.525 141.665 136.904 -5.745 -1.272 1.464  N21 X0O 11 
X0O N23 N2  N 0 1 N N N N N N 132.728 141.433 134.640 -6.229 -2.303 -0.571 N23 X0O 12 
X0O N27 N3  N 0 1 N N N N N N 129.854 143.549 137.076 -4.220 0.500  1.608  N27 X0O 13 
X0O O02 O1  O 0 1 N N N N N N 132.451 143.906 128.573 2.159  2.356  1.244  O02 X0O 14 
X0O O03 O2  O 0 1 N N N N N N 131.592 146.208 128.706 1.194  0.440  2.574  O03 X0O 15 
X0O O04 O3  O 0 1 N N N N N N 134.103 145.793 129.155 2.703  0.018  0.462  O04 X0O 16 
X0O O06 O4  O 0 1 N N N N N N 134.913 147.556 130.856 4.480  -1.158 2.002  O06 X0O 17 
X0O O07 O5  O 0 1 N N N N N N 133.421 148.288 129.041 4.939  1.086  0.940  O07 X0O 18 
X0O O08 O6  O 0 1 N N N N N N 135.868 147.711 128.470 4.923  -0.930 -0.579 O08 X0O 19 
X0O O10 O7  O 0 1 N N N N N N 134.446 147.975 126.328 7.010  0.228  -1.680 O10 X0O 20 
X0O O11 O8  O 0 1 N N N N N N 136.377 146.439 126.278 7.276  -1.604 0.035  O11 X0O 21 
X0O O12 O9  O 0 1 N N N N N N 136.740 148.872 126.346 6.443  -2.275 -2.251 O12 X0O 22 
X0O O13 O10 O 0 1 N N N N N N 132.202 144.977 130.899 0.294  1.033  0.176  O13 X0O 23 
X0O O26 O11 O 0 1 N N N N N N 132.906 140.127 136.729 -7.181 -2.940 1.328  O26 X0O 24 
X0O O28 O12 O 0 1 N N N N N N 130.814 144.465 132.910 -2.445 0.350  -0.559 O28 X0O 25 
X0O O29 O13 O 0 1 N N N N N N 129.732 146.465 135.483 -4.453 2.374  -2.435 O29 X0O 26 
X0O O30 O14 O 0 1 N N N N N N 130.919 147.938 134.197 -2.895 3.886  -1.002 O30 X0O 27 
X0O P01 P1  P 0 1 N N N N N N 132.563 145.221 129.307 1.600  0.991  1.117  P01 X0O 28 
X0O P05 P2  P 0 1 N N N N N N 134.554 147.360 129.403 4.276  -0.217 0.711  P05 X0O 29 
X0O P09 P3  P 0 1 N N N N N N 135.855 147.747 126.822 6.431  -1.155 -1.094 P09 X0O 30 
X0O H1  H1  H 0 1 N N N N N N 133.093 146.127 132.338 -0.493 2.928  0.419  H1  X0O 31 
X0O H2  H2  H 0 1 N N N N N N 132.027 146.997 131.183 -1.245 1.653  1.407  H2  X0O 32 
X0O H3  H3  H 0 1 N N N N N N 130.177 146.423 132.272 -1.461 1.847  -1.641 H3  X0O 33 
X0O H4  H4  H 0 1 N N N N N N 132.554 146.558 134.155 -3.311 2.699  0.658  H4  X0O 34 
X0O H5  H5  H 0 1 N N N N N N 131.596 145.501 135.719 -5.159 1.883  -0.543 H5  X0O 35 
X0O H6  H6  H 0 1 N N N N N N 129.370 144.281 134.261 -3.615 0.097  -2.260 H6  X0O 36 
X0O H7  H7  H 0 1 N N N N N N 134.120 139.883 134.460 -6.395 -4.244 -1.349 H7  X0O 37 
X0O H8  H8  H 0 1 N N N N N N 133.210 140.281 132.963 -7.929 -3.505 -0.830 H8  X0O 38 
X0O H9  H9  H 0 1 N N N N N N 134.508 141.379 133.545 -7.146 -2.968 -2.336 H9  X0O 39 
X0O H10 H10 H 0 1 N N N N N N 132.420 142.672 132.989 -5.226 -1.566 -2.291 H10 X0O 40 
X0O H11 H11 H 0 1 N N N N N N 129.658 143.287 138.021 -3.598 1.103  1.172  H11 X0O 41 
X0O H12 H12 H 0 1 N N N N N N 129.379 144.326 136.664 -4.366 0.563  2.565  H12 X0O 42 
X0O H13 H13 H 0 1 N N N N N N 131.118 145.793 127.995 0.820  -0.452 2.567  H13 X0O 43 
X0O H14 H14 H 0 1 N N N N N N 134.350 148.221 131.235 4.070  -2.030 1.923  H14 X0O 44 
X0O H15 H15 H 0 1 N N N N N N 134.181 147.247 125.777 6.504  0.582  -2.425 H15 X0O 45 
X0O H16 H16 H 0 1 N Y N N N N 137.437 148.520 125.806 7.321  -2.462 -2.609 H16 X0O 46 
X0O H17 H17 H 0 1 N N N N N N 129.324 145.892 136.121 -4.723 3.303  -2.440 H17 X0O 47 
X0O H18 H18 H 0 1 N N N N N N 131.145 148.289 135.050 -3.630 4.501  -0.876 H18 X0O 48 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
X0O O11 P09 DOUB N N 1  
X0O O10 P09 SING N N 2  
X0O O12 P09 SING N N 3  
X0O P09 O08 SING N N 4  
X0O O08 P05 SING N N 5  
X0O O02 P01 DOUB N N 6  
X0O O03 P01 SING N N 7  
X0O O07 P05 DOUB N N 8  
X0O O04 P01 SING N N 9  
X0O O04 P05 SING N N 10 
X0O P01 O13 SING N N 11 
X0O P05 O06 SING N N 12 
X0O O13 C14 SING N N 13 
X0O C14 C15 SING N N 14 
X0O C15 O28 SING N N 15 
X0O C15 C16 SING N N 16 
X0O O28 C18 SING N N 17 
X0O C24 N23 SING N N 18 
X0O C25 N23 SING N N 19 
X0O C25 C19 DOUB N N 20 
X0O C16 O30 SING N N 21 
X0O C16 C17 SING N N 22 
X0O C18 C19 SING N N 23 
X0O C18 C17 SING N N 24 
X0O N23 C22 SING N N 25 
X0O C19 C20 SING N N 26 
X0O C17 O29 SING N N 27 
X0O C22 O26 DOUB N N 28 
X0O C22 N21 SING N N 29 
X0O C20 N21 DOUB N N 30 
X0O C20 N27 SING N N 31 
X0O C14 H1  SING N N 32 
X0O C14 H2  SING N N 33 
X0O C15 H3  SING N N 34 
X0O C16 H4  SING N N 35 
X0O C17 H5  SING N N 36 
X0O C18 H6  SING N N 37 
X0O C24 H7  SING N N 38 
X0O C24 H8  SING N N 39 
X0O C24 H9  SING N N 40 
X0O C25 H10 SING N N 41 
X0O N27 H11 SING N N 42 
X0O N27 H12 SING N N 43 
X0O O03 H13 SING N N 44 
X0O O06 H14 SING N N 45 
X0O O10 H15 SING N N 46 
X0O O12 H16 SING N N 47 
X0O O29 H17 SING N N 48 
X0O O30 H18 SING N N 49 
# 
loop_
_pdbx_chem_comp_descriptor.comp_id 
_pdbx_chem_comp_descriptor.type 
_pdbx_chem_comp_descriptor.program 
_pdbx_chem_comp_descriptor.program_version 
_pdbx_chem_comp_descriptor.descriptor 
X0O InChI            InChI                1.06  "InChI=1S/C10H18N3O14P3/c1-13-2-4(9(11)12-10(13)16)8-7(15)6(14)5(25-8)3-24-29(20,21)27-30(22,23)26-28(17,18)19/h2,5-8,14-15H,3H2,1H3,(H,20,21)(H,22,23)(H2,11,12,16)(H2,17,18,19)/t5-,6-,7-,8+/m1/s1" 
X0O InChIKey         InChI                1.06  JCPRKVWIOJLDIF-XUTVFYLZSA-N                                                                                                                                                                           
X0O SMILES_CANONICAL CACTVS               3.385 "CN1C=C([C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O)C(=NC1=O)N"                                                                                                                
X0O SMILES           CACTVS               3.385 "CN1C=C([CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O)C(=NC1=O)N"                                                                                                                      
X0O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1C=C(C(=NC1=O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                    
X0O SMILES           "OpenEye OEToolkits" 2.0.7 "CN1C=C(C(=NC1=O)N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O"                                                                                                                                      
# 
_pdbx_chem_comp_identifier.comp_id           X0O 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "[[(2~{R},3~{S},4~{R},5~{S})-5-(4-azanyl-1-methyl-2-oxidanylidene-pyrimidin-5-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
X0O "Create component" 2023-05-25 RCSB 
X0O "Initial release"  2023-12-27 RCSB 
# 
